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At lower temperatures, there is usually not enough energy to overcome an activation energy barrier, so the pathway that has the smaller activation energy will be the faster reaction and the one that is observed. This is kinetically determined. This is also different than reactions that are spontaneous, because that is driven by thermodynamics. Spontaneous reactions can still eons and eons to happen.
Activation energy has to do with kinetics. Thermodynamics is concerned with the difference in internal energy before and after the reaction, which is a different concept, and mathematical value from the activation energy for the same reaction.
Activation energy is the main determinant in the kinetic stability of a reaction. For instance, a reaction is kinetically stable if the activation energy is exceedingly high (i.e.; the conversion of carbon (diamond) into carbon (graphite) since said reaction would take a high amount of energy to undergo. Thermodynamic stability refers to whether the reaction is spontaneous or not with regards to the Gibbs free energy of a reaction, not necessarily the activation energy.
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